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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Cavity similarities measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Cavities are compared using Shaper.
For more information, please see the following publication: Desaphy J. et al. Comparison and Druggability Prediction of protein-Ligand Binding sites from pharmacophore-annotated cavity shapes J. Chem. Inf. Model., 2012, 52(8), pp2287-2299

Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
5hbsRTLRetinol-binding protein 1

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
5hbsRTLRetinol-binding protein 1/1.000
5h8tRTLRetinol-binding protein 1/0.644
1crbRTLRetinol-binding protein 1/0.626
1opbRETRetinol-binding protein 2/0.579
1kqwRTLCellular retinol-binding protein type II/0.562
5k2cZMAAdenosine receptor A2a/0.510
3gytDL4Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.508
5iubCLRAdenosine receptor A2a/0.507
5iu86DZAdenosine receptor A2a/0.503
2po7CHDFerrochelatase, mitochondrial4.99.1.10.501
3emlZMAAdenosine receptor A2a/0.500
5iu4ZMAAdenosine receptor A2a/0.498
5k2bZMAAdenosine receptor A2a/0.498
4i6h1C8Serine/threonine-protein kinase PLK22.7.11.210.497
3up0D7SaceDAF-12/0.496
3reyXACAdenosine receptor A2a/0.496
3nrrD16Bifunctional dihydrofolate reductase-thymidylate synthase/0.494
5g53NECAdenosine receptor A2a/0.492
4i6f1C7Serine/threonine-protein kinase PLK22.7.11.210.490
5k2aZMAAdenosine receptor A2a/0.489
3nmpPYVAbscisic acid receptor PYL2/0.486
4qzuRTLRetinol-binding protein 2/0.486
3djlFADPutative acyl-CoA dehydrogenase AidB1.3.990.485
5jtbZMAAdenosine receptor A2a/0.485
4bb5HD2Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.482
5gcnCOAHAT A1/0.482
4eiyZMAAdenosine receptor A2a/0.481
5uviZMAAdenosine receptor A2a/0.481
3ns2PYVAbscisic acid receptor PYL2/0.480
3oezSTIProto-oncogene tyrosine-protein kinase Src2.7.10.20.478
5k2dZMAAdenosine receptor A2a/0.478
3nj0PYVAbscisic acid receptor PYL2/0.477
4kwi1TJReductase homolog/0.477
2g78REACellular retinoic acid-binding protein 2/0.476
3gyuDL7Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.476
2hl2SSAThreonine--tRNA ligase6.1.1.30.475
3uleC69Actin-related protein 3/0.475
1bvrNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.474
2z3uCRRCytochrome P450/0.474
3l0lHC3Nuclear receptor ROR-gamma/0.474
3tm5SFGUncharacterized protein/0.474
5iua6DXAdenosine receptor A2a/0.473
1d3hA26Dihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.472
2xk730ESerine/threonine-protein kinase Nek22.7.11.10.472
3gwfNAPCyclohexanone monooxygenase/0.472
3lfcZ86Mitogen-activated protein kinase 14/0.472
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.471
1lriCLRBeta-elicitin cryptogein/0.471
3cd2MTXDihydrofolate reductase1.5.1.30.471
4j6cSTRCytochrome P450 monooxygenase/0.471
3czr3CZCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.470
3g49NAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.470
3njoPYVAbscisic acid receptor PYR1/0.470
2aibERGBeta-elicitin cinnamomin/0.469
2h2qNAPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.469
3vg9ZMAAdenosine receptor A2a/0.469
4tzt468Enoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.469
3h3r14HCollagen type IV alpha-3-binding protein/0.468
4nb6444Nuclear receptor ROR-gamma/0.468
3qakUKAAdenosine receptor A2a/0.468
1og5SWFCytochrome P450 2C9/0.467
1cbqRE9Cellular retinoic acid-binding protein 2/0.466
1fmjRTLRetinol dehydratase/0.466
1ly4COQDihydrofolate reductase1.5.1.30.466
3up3XCAaceDAF-12/0.466
3uwlFOZThymidylate synthase/0.466
1fpqSAMIsoliquiritigenin 2'-O-methyltransferase/0.465
2vcmM11Isopenicillin N synthase1.21.3.10.465
3a1l2CCCytochrome P450/0.465
2bakAQZMitogen-activated protein kinase 14/0.464
4a9yAQZMitogen-activated protein kinase 14/0.464
4ckrDI1Epithelial discoidin domain-containing receptor 12.7.10.10.464
3hcrCHDFerrochelatase, mitochondrial4.99.1.10.463
4dquNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.463
4em3FADCoenzyme A disulfide reductase/0.463
2qx7NAPEugenol synthase 11.1.1.3180.462
2wsa646Glycylpeptide N-tetradecanoyltransferase/0.462
3a783EVVitamin D3 receptor/0.462
3csdEMOPutative ketoacyl reductase1.3.10.462
3jwcEKBDihydrofolate reductase/0.462
3ua506XCytochrome P450 2B61.14.130.462
4ku5DCC3-oxoacyl-[ACP] synthase III/0.462
3uzcT4EAdenosine receptor A2a/0.462
1juvNDPDihydrofolate reductase1.5.1.30.461
1oc1ASVIsopenicillin N synthase1.21.3.10.461
4a2aATPCell division protein FtsA/0.461
2djiFADPyruvate oxidase/0.460
3qrwNDPPutative ketoacyl reductase1.3.10.460
4j6dTESCytochrome P450 monooxygenase/0.460
4klrCHDFerrochelatase, mitochondrial4.99.1.10.460
5i2hAGIO-methyltransferase family 2/0.460
1dd6MCIMetallo-beta-lactamase type 2/0.459
1dfoFFOSerine hydroxymethyltransferase2.1.2.10.459
1oriSAHProtein arginine N-methyltransferase 1/0.459
2w3vTOPDihydrofolate reductase/0.459
3dhcCYKN-acyl homoserine lactonase AiiA3.1.1.810.459
3sp9IL2Peroxisome proliferator-activated receptor delta/0.459
4dscA8SAbscisic acid receptor PYL3/0.459
4twnB96Ephrin type-A receptor 32.7.10.10.459
1cbsREACellular retinoic acid-binding protein 2/0.458
1ju6LYAThymidylate synthase2.1.1.450.458
1qiqACCIsopenicillin N synthase1.21.3.10.458
3kjsDQ1Bifunctional dihydrofolate reductase-thymidylate synthase/0.458
3zkyWT4Isopenicillin N synthase1.21.3.10.458
4h6rFDAProline dehydrogenase/0.458
1v5eFADPyruvate oxidase/0.457
3dxjNE6DNA-directed RNA polymerase subunit beta/0.457
3dxjNE6DNA-directed RNA polymerase subunit beta'/0.457
3vt45YIVitamin D3 receptor/0.457
1e90MYCPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.456
1uuoBRFDihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.456
3irm1CYBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.456
3ozd4CTS-methyl-5'-thioadenosine phosphorylase/0.456
4caxMYAGlycylpeptide N-tetradecanoyltransferase2.3.1.970.456
4qe6JN3Bile acid receptor/0.456
4uhrNGIAdenosine receptor A2a/0.456
1kzjCB3Thymidylate synthase/0.455
2ftoCB3Thymidylate synthase/0.455
2pv7NADT-protein1.3.1.120.455
2r6jNDPEugenol synthase 11.1.1.3180.455
3a4oSTUTyrosine-protein kinase Lyn2.7.10.20.455
3e92G6AMitogen-activated protein kinase 14/0.455
3gkjHC3Niemann-Pick C1 protein/0.455
3kpzZNEVitamin D3 receptor/0.455
3um61CYBifunctional dihydrofolate reductase-thymidylate synthase/0.455
4j6bPLOCytochrome P450 monooxygenase/0.455
1blzACVIsopenicillin N synthase1.21.3.10.454
2aq7TL53-oxoacyl-[acyl-carrier-protein] synthase 12.3.1.410.454
2jlaTPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.454
2xkdT3MSerine/threonine-protein kinase Nek22.7.11.10.454
2ydoADNAdenosine receptor A2a/0.454
3g4gD71cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.454
3glmCOOGlutaconyl-CoA decarboxylase alpha subunit/0.454
4cavMYAGlycylpeptide N-tetradecanoyltransferase2.3.1.970.454
1f5fDHTSex hormone-binding globulin/0.453
2jfaRALEstrogen receptor/0.453
3nmhPYVAbscisic acid receptor PYL2/0.453
3nwlNDPCatalase1.11.1.60.453
3zu2NAIEnoyl-[acyl-carrier-protein] reductase [NADH]/0.453
4a2bAGSCell division protein FtsA/0.453
1bifAGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 42.7.1.1050.452
1sqvUHDCytochrome b/0.452
1uioHPRAdenosine deaminase3.5.4.40.452
2f2sCOAAcetyl-CoA acetyltransferase, mitochondrial2.3.1.90.452
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.452
3vt7VDXVitamin D3 receptor/0.452
3w8wFADPutative FAD-dependent oxygenase EncM/0.452
4a9mP9MBromodomain-containing protein 2/0.452
4ezk0SDPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.452
4jvb1M0Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.452
1d3gBREDihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.451
1j3kWRABifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.451
1ly3COGDihydrofolate reductase1.5.1.30.451
1osvCHCBile acid receptor/0.451
2bfmTOPPteridine reductase 11.5.1.330.451
3deiRXBCaspase-33.4.22.560.451
3g70A5TRenin3.4.23.150.451
3qlrNDPDihydrofolate reductase1.5.1.30.451
3w0aDS5Vitamin D3 receptor/0.451
5c6cCMPcGMP-dependent protein kinase 22.7.11.120.451
8catNDPCatalase1.11.1.60.451
1fm7DFVChalcone--flavonone isomerase 15.5.1.60.450
1jujLYAThymidylate synthase2.1.1.450.450
1nzdUPGDNA beta-glucosyltransferase/0.450
1tl7ONMAdenylate cyclase type 2/0.450
1tl7ONMAdenylate cyclase type 5/0.450
2aqhNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.450
2wesFADTryptophan 5-halogenase/0.450
2wo7ASVIsopenicillin N synthase1.21.3.10.450
3ac1KZITyrosine-protein kinase Lck2.7.10.20.450
3dxmN24Actin-related protein 3/0.450
3i6qNDPPutative leucoanthocyanidin reductase 1/0.450
3ictADPCoenzyme A disulfide reductase/0.450
3td8D2RDihydrofolate reductase1.5.1.30.450
3tqhNDPQuinone oxidoreductase/0.450
3v49PK0Androgen receptor/0.450
3w1wCHDFerrochelatase, mitochondrial4.99.1.10.450
3wv7ADPHmd co-occurring protein HcgE/0.450
4ajfF03cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.450
4g20484Vitamin D3 receptor A/0.450
4ie0PD2Alpha-ketoglutarate-dependent dioxygenase FTO/0.450
4imfSI3N-acetylneuraminate lyase/0.450
4l8u9AZSerum albumin/0.450
4yekTHMThymidine phosphorylase/0.450
1ddtAPUDiphtheria toxin/0.449
1ikwEFZGag-Pol polyprotein2.7.7.490.449
1s19MC9Vitamin D3 receptor/0.449
2v1aFMNNPH1-1/0.449
3kjsNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.449
3wmxNADNAD dependent epimerase/dehydratase/0.449
4jv81M1Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.449
4rupH97Vitamin D3 receptor A/0.449
5eccNAPDehydrofolate reductase type I/0.449
1dggNDPCatalase1.11.1.60.448
1jpaANPEphrin type-B receptor 22.7.10.10.448
1o5rFR9Adenosine deaminase3.5.4.40.448
1rk3VDXVitamin D3 receptor/0.448
1so2666cGMP-inhibited 3',5'-cyclic phosphodiesterase B3.1.4.170.448
1txtCAAHMG-CoA synthase/0.448
2hb7O1CVitamin D3 receptor/0.448
2xkeWI2Serine/threonine-protein kinase Nek22.7.11.10.448
3el7PD3Proto-oncogene tyrosine-protein kinase Src2.7.10.20.448
3hk1B64Fatty acid-binding protein, adipocyte/0.448
3njoP2MAbscisic acid receptor PYR1/0.448
4egnTWOCytochrome P450/0.448
4g1y0VOVitamin D3 receptor A/0.448
4h3j10WBeta-secretase 13.4.23.460.448
4j531J4Serine/threonine-protein kinase PLK12.7.11.210.448
4qemHC4Phospholipase A2 VRV-PL-VIIIa/0.448
2blcCP7Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.447
2hb8MVDVitamin D3 receptor/0.447
2p15EZTEstrogen receptor/0.447
2rl52RLVascular endothelial growth factor receptor 22.7.10.10.447
2ydvNECAdenosine receptor A2a/0.447
2zevB71Geranylgeranyl pyrophosphate synthase/0.447
3cz09ODPheromone-binding protein ASP1/0.447
3gb4D3MDdmC/0.447
4nky3QZSteroid 17-alpha-hydroxylase/17,20 lyase/0.447
1ie9VDXVitamin D3 receptor/0.446
1jtuLYBThymidylate synthase/0.446
1kkq471Peroxisome proliferator-activated receptor alpha/0.446
1wsvTHHAminomethyltransferase, mitochondrial/0.446
1xu9CPSCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.446
1z6lFADPolyamine oxidase FMS1/0.446
2in6839Wee1-like protein kinase2.7.10.20.446
2kceD16Thymidylate synthase/0.446
2o4rVD5Vitamin D3 receptor/0.446
2rehFADNitroalkane oxidase1.7.3.10.446
3c3eGDP2-phospho-L-lactate transferase/0.446
3cbsR12Cellular retinoic acid-binding protein 2/0.446
3d78NBBPheromone-binding protein ASP1/0.446
3nxvD2FDihydrofolate reductase1.5.1.30.446
4bkjSTIEpithelial discoidin domain-containing receptor 12.7.10.10.446
4dc0NDPPutative ketoacyl reductase1.3.10.446
4fhh0U3Vitamin D3 receptor A/0.446
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
4jqh1MFAlr2278 protein/0.446
4jvf17XRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.446
4oj4DIFPeroxisome proliferator-activated receptor gamma/0.446
4r20AERCytochrome P450 family 17 polypeptide 2/0.446
4qinSG8Smoothened homolog/0.446
3pwhZMAAdenosine receptor A2a/0.446
1bi9NADRetinal dehydrogenase 2/0.445
1ia4TQ6Dihydrofolate reductase1.5.1.30.445
1upw444Oxysterols receptor LXR-beta/0.445
2c59NADGDP-mannose 3,5-epimerase5.1.3.180.445
3adaNADSubunit alpha of sarocosine oxidase/0.445
3bi6396Wee1-like protein kinase2.7.10.20.445
3iro2CYBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.445
3vt5YI2Vitamin D3 receptor/0.445
3vt65YIVitamin D3 receptor/0.445
3vtdTKDVitamin D3 receptor/0.445
4a30QMIGlycylpeptide N-tetradecanoyltransferase/0.445
4bbxLKFcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.445
4do30LAFatty-acid amide hydrolase 13.5.1.990.445
4knzCB3Thymidylate synthase/0.445
4v12POGMaoC like domain protein/0.445
1s6qTPBGag-Pol polyprotein2.7.7.490.444
2bnsMSTReaction center protein L chain/0.444
2cahNDPCatalase1.11.1.60.444
2gvcFADThiol-specific monooxygenase1.14.130.444
2i0ePDSProtein kinase C beta type2.7.11.130.444
2ociTYCValacyclovir hydrolase3.10.444
2vbpVB1Isopenicillin N synthase1.21.3.10.444
2y6fM9FIsopenicillin N synthase1.21.3.10.444
2ynfWHUGag-Pol polyprotein2.7.7.490.444
3c1xCKKHepatocyte growth factor receptor2.7.10.10.444
3dejRXCCaspase-33.4.22.560.444
3v1uHXC3-oxoacyl-(Acyl-carrier-protein) reductase/0.444
4a4l939Serine/threonine-protein kinase PLK12.7.11.210.444
4bb6HD1Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.444
4bvaT3Ketimine reductase mu-crystallin1.5.1.250.444
5cpbNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.444
5hwqCAAHydroxymethylglutaryl-CoA synthase/0.444
1ejiTHFSerine hydroxymethyltransferase, cytosolic/0.443
1kt3RTLRetinol-binding protein 4/0.443
1m67BOAGlycerol-3-phosphate dehydrogenase [NAD(+)], glycosomal1.1.1.80.443
2j3jHC4NADPH-dependent oxidoreductase 2-alkenal reductase1.3.1.740.443
3hub469Mitogen-activated protein kinase 14/0.443
3llaACPMyosin heavy chain kinase A2.7.11.70.443
3mdvCL6Cholesterol 24-hydroxylase/0.443
3ml8ML8Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.443
3qlzQLZUncharacterized protein/0.443
3sfi3SFHTH-type transcriptional regulator EthR/0.443
3vt9YI4Vitamin D3 receptor/0.443
3vtbTKAVitamin D3 receptor/0.443
3w0gW07Vitamin D3 receptor/0.443
3w0pADPHygromycin-B 4-O-kinase2.7.1.1630.443
4c2jCOA3-ketoacyl-CoA thiolase, mitochondrial2.3.1.160.443
4dw60MNHTH-type transcriptional regulator EthR/0.443
4llkMEWcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.443
4pkl1GHUncharacterized protein/0.443
4rd2GNPTranslation initiation factor 2 subunit gamma/0.443
3uzaT4GAdenosine receptor A2a/0.443
1e1kNAPNADPH:adrenodoxin oxidoreductase, mitochondrial1.18.1.60.442
1jlaTNKGag-Pol polyprotein2.7.7.490.442
1pq944BOxysterols receptor LXR-beta/0.442
1szmBI4cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.442
2pg0FADAcyl-CoA dehydrogenase/0.442
2r0pK2CPutative FAD-monooxygenase/0.442
2z2w770Wee1-like protein kinase2.7.10.20.442
3b9lAZZSerum albumin/0.442
3d75NBBPheromone-binding protein ASP1/0.442
3d84NDPDihydrofolate reductase1.5.1.30.442
3nguADPNucleoside diphosphate kinase/0.442
3tvxPNXcAMP-specific 3',5'-cyclic phosphodiesterase 4A3.1.4.530.442
4bqpNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.442
4fnyI3KALK tyrosine kinase receptor2.7.10.10.442
4gncASORegucalcin3.1.1.170.442
7catNDPCatalase1.11.1.60.442
4ug2NGIAdenosine receptor A2a/0.442
1qknRALEstrogen receptor beta/0.441
1rjkVDZVitamin D3 receptor/0.441
2aazCB3Thymidylate synthase2.1.1.450.441
2acwUPGGlycosyltransferase/0.441
2bf7HBIPteridine reductase 11.5.1.330.441
2j5xGSPADP-ribosylation factor 6/0.441
2wkyIBCGlutamate receptor ionotropic, kainate 1/0.441
3kytHC2Nuclear receptor ROR-gamma/0.441
3qm4PN0Cytochrome P450 2D6/0.441
3vi5M4MHematopoietic prostaglandin D synthase/0.441
3vtcTK3Vitamin D3 receptor/0.441
3wv9FEGHmd co-occurring protein HcgE/0.441
4a06ATP3-phosphoinositide-dependent protein kinase 12.7.11.10.441
4alhA9PBromodomain-containing protein 2/0.441
4cs0ACOPanD regulatory factor/0.441
4itfTFYVitamin D3 receptor/0.441
5dq8FLFTranscriptional enhancer factor TEF-4/0.441
1enyNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.440
1fm4DXCMajor pollen allergen Bet v 1-L/0.440
1txzAPRProbable ADP-ribose 1''-phosphate phosphatase YML087W3.1.3.840.440
1zsnTN2Enoyl-ACP reductase/0.440
2cig1DGDihydrofolate reductase1.5.1.30.440
2gtmLIDMitogen-activated protein kinase 14/0.440
2idzZIDEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.440
2ourCMPcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.440
2prh238Dihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.440
2uxhQUEHTH-type transcriptional regulator TtgR/0.440
2weyEV1cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.440
3bx5304Mitogen-activated protein kinase 14/0.440
3cgcCOACoenzyme A disulfide reductase/0.440
3fl4FL4Mitogen-activated protein kinase 14/0.440
3gc9B45Mitogen-activated protein kinase 112.7.11.240.440
3ocpCMPcGMP-dependent protein kinase 12.7.11.120.440
3zbnCOA3-ketoacyl-CoA thiolase-like protein/0.440
4elb34SDihydrofolate reductase/0.440
4fad0TBPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.440
4fgh0U6Dihydrofolate reductase1.5.1.30.440
4g1z0VPVitamin D3 receptor A/0.440